TNG (the series with which I am most fond of and familiar) presented dozens of excellent and intricate moral challenges throughout it's run. Did Data fire on Kivas Fajo or not in The Most Toys? What about the attack on religion as portrayed in Who Watches the Watchers? When Dr. Marr destroys the crystilline entity in Silicon Avatar, is Picard right to try and stop her? Then there are the what-constitutes-sentience as explored in both The Measure of a Man and The Offspring. Nearly every episode comes loaded with some form of philosophical material for reflection.
There's not a question about Data firing at Fajo - we saw him do it, and then lie about it.
Most of these examples aren't at all intricate or challenging - they were pretty simplistic put-up jobs. No one watching the show really sympathizes with the argument that Data or his daughter aren't sentient beings who should have rights, for example - or, at least, so few viewers do that it's of no importance (I mean, I'm sure there are a few folks watching things like Psycho
who identify with Norman Bates, too).